Protein structure comparison basis on structural classification information

PSAML (Protein Structure Abstraction Markup Language) is a protein data model which describes a protein structure as its secondary structure elements and their relationships. SCOP (Structural Classification Of Proteins) is a database storing structural classification of proteins whose three-dimensional structures have been determined. In this paper, we present a new method of comparing two protein structures described in PSAML and a way of finding similar substructures on the basis of structural classification of proteins. With the help of the extracted SCOP classification information, we efficiently decreased the number of candidate protein structures to be compared.